WEIGHTED ALIGNMENT FREE DISSIMILARITY METRIC FOR PROMOTER SEQUENCE COMPARISON
نویسندگان
چکیده
منابع مشابه
Multiple alignment-free sequence comparison
MOTIVATION Recently, a range of new statistics have become available for the alignment-free comparison of two sequences based on k-tuple word content. Here, we extend these statistics to the simultaneous comparison of more than two sequences. Our suite of statistics contains, first, C(*)1 and C(S)1, extensions of statistics for pairwise comparison of the joint k-tuple content of all the sequenc...
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MOTIVATION Genetic recombination and, in particular, genetic shuffling are at odds with sequence comparison by alignment, which assumes conservation of contiguity between homologous segments. A variety of theoretical foundations are being used to derive alignment-free methods that overcome this limitation. The formulation of alternative metrics for dissimilarity between sequences and their algo...
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BACKGROUND Existing sequence alignment algorithms use heuristic scoring schemes based on biological expertise, which cannot be used as objective distance metrics. As a result one relies on crude measures, like the p- or log-det distances, or makes explicit, and often too simplistic, a priori assumptions about sequence evolution. Information theory provides an alternative, in the form of mutual ...
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In this paper, we propose to learn a Mahalanobis distance to perform alignment of multivariate time series. The learning examples for this task are time series for which the true alignment is known. We cast the alignment problem as a structured prediction task, and propose realistic losses between alignments for which the optimization is tractable. We provide experiments on real data in the aud...
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Rapid methods for alignment-free sequence comparison make large-scale comparisons between sequences increasingly feasible. Here we study the power of the statistic D2, which counts the number of matching k-tuples between two sequences, as well as D2*, which uses centralized counts, and D2S, which is a self-standardized version, both from a theoretical viewpoint and numerically, providing an eas...
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ژورنال
عنوان ژورنال: International Journal for Computational Biology
سال: 2015
ISSN: 2278-8115
DOI: 10.34040/ijcb.4.2.2015.56